Mon Oct 10 17:04:06 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:04:06 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2992 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5331496 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -31.79700 34.97600 ymin,ymax (A): -23.22500 25.56800 zmin,zma (A): -7.873000 40.37100 x,y,z range (A): 66.77300 48.79300 48.24400 scale (grids/A): 0.5331496 object centre (A): 1.589501 1.171499 16.24900 number of atom coordinates read : 2992 total number of charged atoms : 2851 net assigned charge : -4.471962 assigned positive charge : 452.5118 centred at (gu) : 90.54110 90.65414 89.60247 assigned negative charge : -456.9850 centred at (gu) : 90.61832 90.54340 89.55386 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5647 nv = 96 ne = 84 npr = 58480 no. pairs analyzed = 58480 no. exposed pairs = 4067 no. arc points = 28674 no. surface atoms = 1359 nbur = 1633 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 237 mr = 2820 m= 0 mr = 8 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3100000 number of dielectric boundary points 3056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2871 ## 427 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7370 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1020387E-10 3.1180825E-11 midg,1,midg; midg,igrid,midg -5.3881744E-10 3.4442921E-10 1,midg,midg; igrid,midg,midg 1.3220879E-10 -5.6513905E-10 gauss-seidel spectral radius is 0.9818795 estimated iterations to convergence 61 setup time was (sec) 0.5200000 now iterating at: 17:04:06 rms-change max change #iterations 6.5653034E-02 12.16764 at 10iterations 4.0841051E-03 0.7415848 at 20iterations 2.5334954E-04 4.3228149E-02 at 30iterations 1.6258526E-05 3.3559799E-03 at 40iterations 1.0646164E-06 1.7786026E-04 at 50iterations finished qdiffx linear iterations at : 17:04:09 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.0646164E-06 1.7786026E-04 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 17:04:11 3.125u 0.164s 0:04.99 65.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:04:11 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2992 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.599449 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -31.79700 34.97600 ymin,ymax (A): -23.22500 25.56800 zmin,zma (A): -7.873000 40.37100 x,y,z range (A): 66.77300 48.79300 48.24400 scale (grids/A): 1.599449 object centre (A): 1.589501 1.171499 16.24900 number of atom coordinates read : 2992 total number of charged atoms : 2851 net assigned charge : -4.471962 assigned positive charge : 452.5118 centred at (gu) : 91.62234 91.96152 88.80652 assigned negative charge : -456.9850 centred at (gu) : 91.85464 91.62991 88.66130 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28674 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19317 mr = 41786 m= 1902 mr = 13028 m= 51 mr = 849 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 713 time to turn everything in is 0.4500000 number of dielectric boundary points 28423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 353 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 21712 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5331496 object centre at (A) : 1.589501 1.171499 16.24900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4982846E-03 -1.5694414E-03 midg,1,midg; midg,igrid,midg -9.9690119E-03 5.6862962E-03 1,midg,midg; igrid,midg,midg -4.7740145E-03 -2.3215903E-02 gauss-seidel spectral radius is 0.9981120 estimated iterations to convergence 183 setup time was (sec) 0.7200000 now iterating at: 17:04:11 rms-change max change #iterations 3.207170 149.5218 at 10iterations 1.300504 53.48516 at 20iterations 0.5319350 20.37592 at 30iterations 0.2182436 8.120423 at 40iterations 8.9075558E-02 3.501804 at 50iterations 3.6458310E-02 1.462572 at 60iterations 1.4933767E-02 0.6101518 at 70iterations 6.1087231E-03 0.2357941 at 80iterations 2.5099413E-03 9.0753555E-02 at 90iterations 1.0293687E-03 3.9809227E-02 at 100iterations 4.2305264E-04 1.7274737E-02 at 110iterations 1.7308723E-04 7.2021484E-03 at 120iterations finished qdiffx linear iterations at : 17:04:18 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 1.7308723E-04 7.2021484E-03 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 17:04:19 6.936u 0.159s 0:08.12 87.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:04:19 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2992 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.399173 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -31.79700 34.97600 ymin,ymax (A): -23.22500 25.56800 zmin,zma (A): -7.873000 40.37100 x,y,z range (A): 66.77300 48.79300 48.24400 scale (grids/A): 2.399173 object centre (A): 1.589501 1.171499 16.24900 number of atom coordinates read : 2992 total number of charged atoms : 2851 net assigned charge : -4.471962 assigned positive charge : 452.5118 centred at (gu) : 92.43341 92.94215 88.20956 assigned negative charge : -456.9850 centred at (gu) : 92.78181 92.44478 87.99185 start vw surface at 0.1700000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 145855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28674 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 67202 mr = 102512 m= 18829 mr = 52534 m= 2788 mr = 13869 m= 163 mr = 1724 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2664 time to turn everything in is 1.060000 number of dielectric boundary points 64156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 22770 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.599449 object centre at (A) : 1.589501 1.171499 16.24900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4528652E-02 -4.1126478E-02 midg,1,midg; midg,igrid,midg -0.1397376 0.1120288 1,midg,midg; igrid,midg,midg -3.2402392E-02 -0.6506844 gauss-seidel spectral radius is 0.9991196 estimated iterations to convergence 266 setup time was (sec) 1.340000 now iterating at: 17:04:21 rms-change max change #iterations 8.565559 268.9394 at 10iterations 4.794097 119.7767 at 20iterations 2.658284 61.21961 at 30iterations 1.473857 33.14692 at 40iterations 0.8120670 18.50274 at 50iterations 0.4453292 10.00965 at 60iterations 0.2449122 5.102318 at 70iterations 0.1340286 2.994952 at 80iterations 7.3408835E-02 1.664209 at 90iterations 4.0134534E-02 0.8442078 at 100iterations 2.1888686E-02 0.5264435 at 110iterations 1.1976962E-02 0.2420063 at 120iterations 6.5437262E-03 0.1473331 at 130iterations 3.5624632E-03 8.1287384E-02 at 140iterations 1.9460729E-03 5.1692963E-02 at 150iterations 1.0631990E-03 2.3399353E-02 at 160iterations 5.7924073E-04 1.2390137E-02 at 170iterations 3.1554580E-04 6.7787170E-03 at 180iterations finished qdiffx linear iterations at : 17:04:30 total time elapsed so far: 10.56000 # loops : 180 mean,max change (kT/e) : 3.1554580E-04 6.7787170E-03 energy calculations done at 10.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.74000 DelPhi exited at 17:04:31 10.746u 0.162s 0:11.73 92.9% 0+0k 0+0io 0pf+0w